The association between the MS499 genome and the phylogroup B1 or ExPECs groups. The scale to the left of the image describes the colours which indicate a difference in frequency between the phylogroup B1 group (−100 to < 0, blue) and ExPEC group ( > 0 to +100, red). These colours are used to represent query windows across the length of the MS499 chromosome (a) and plasmid (b), where regions more frequently found in ExPECs than B1s are red, regions of no difference between the two groups are white, while regions more frequently found in B1s than ExPECs are blue. Significance values on the y-axis are the results of two-tailed Fisher’s exact test to determine whether a query window is significantly associated with either group, and the results for each query window are represented on the graph by semi-transparent grey circles (where circles overlap, these appear darker). Regions of DNA which appear white in the main panel do not differentiate between query windows which are uniformly common or uniformly rare, therefore the line graphs presented above the main panels track the frequency of each window in the B1 group (blue line) and ExPEC group (red line) independently. These data indicate that approximately 4% of the MS499 chromosome (within 52 contiguous regions) and 52% of the putative MS499 plasmid (within 10 contiguous regions) are significantly associated with the ExPEC group (p = < 0.0000021 for the chromosome, < 0.00007 for the plasmid).